# This file lists all ddG values for mutations to E. coli thioredoxin that I was able to find.  The
# exception to this is that I have excluded ddG values for mutations to active site residues or
# residues that are known to be crucially involved in function.  The reason is that these mutations
# may be thermodynamically stabilizing, but selected against by functional pressures.  The
# ddG values are for free energies of folding, so a positive ddG value indicates a destabilizing
# mutation.  All ddG values given below are in units of kcal/mol.  Each ddG value is preceded by 
# the reference from with it was taken.  
#
# [1] HW Hellinga, R Wynn, and FM Richards. "The hydrophobic core of Escherichia coli 
#       thioredoxin shows a high tolerance to nonconservative single amino acid substitutions."
#       Biochemistry, 31:11203-11209 (1992).  This reference measures mutations by GuHCl chemical
#       denaturation.  It measures a free energy of folding of -13.6 kcal/mol for wildtype.
#       The ddG values are taken from Table II.
L78K    3.9
L78R    4.5
L78D    4.9
L78E    3.1
L42E    3.8
#
# [2] R Godoy-Ruiz, R Perez-Jimenez, B Ibarra-Molero, and JM Sanchez-Ruiz. "Relation between 
#       protein stability, evolution and structure as probed by carboxylic acid mutations."
#       J Mol Biol, 336:313-318 (2004).  Stabilities were measured by DSC.  The reference does 
#       not give the actual numerical values of the ddG values, so they were eye-balled from 
#       Figure 1.  Note that reference [4] does report numerical values for ddG values for these
#       same mutations (in supporting information) calculated using chemical denaturation, 
#       but I have chosen to use the eye-balled values from Figure 1 of this reference since 
#       the DSC values are probably more accurate.  Note that Figure 1 gives the values in kJ/mol,
#       I have converted them to kcal/mol.  I have also converted them to free energy of folding
#       values (they are reported as free energy of unfolding).  The conversion was made using
#       1 kJ/mol = 0.24 kcal/mol.
D2E 0.2
D9E 0.8
D10E    0.0
D13E    -0.2
E30D    0.3
D43E    -0.2
E44D    1.0
D47E    -0.4
E48D    1.3
D61E    0.3
E85D    1.0
E101D   0.6
D104E   0.4
#
# [3] R Godoy-Ruiz, R Perez-Jimenez, B Ibarra-Molero, and JM Sanchez-Ruiz. "A stability pattern 
#       of protein hydrophobic mutations that reflects evolutionary structural optimization."
#       Biophysical J, 89:3320-3331 (2005).  Stabilities were measured by DSC.  The reference does
#       not give the actual numerical values of the ddG values, so they were eye-balled from 
#       Figure 1.  Note that reference [4] does report numerical values for ddG values for these
#       same mutations (in supporting information) calculated using chemical denaturation, 
#       but I have chosen to use the eye-balled values from Figure 1 of this reference since 
#       the DSC values are probably more accurate.  Note that Figure 1 gives the values in kJ/mol,
#       I have converted them to kcal/mol.  I have also converted them to free energy of folding
#       values (they are reported as free energy of unfolding).  The conversion was made using 
#       1 kJ/mol = 0.24 kcal/mol
I4V 0.1
I5V 0.6
V16I    0.6
I23V    -0.3
V25I    0.8
I38V    0.8
I41V    0.5
I45V    0.9
V55I    0.3
I60V    0.2
I72V    -0.1
I75V    0.0
V86I    0.4
V91I    0.3
#
# [4] R Godoy-Ruiz, F Ariza, D Rodriguez-Larrea, R Perez-Jimenez, B Ibarra-Molero, and JM Sanchez-Ruiz.
#       "Natural selection for kinetic stability is a likely origin of correlations between mutational
#       effects on protein energetics and frequencies of amino acid occurrences in sequence alignments."
#       J Mol Biol. 362:966-978 (2006).  This reference again gives the ddG values listed above from
#       references [2] and [3].  It also lists ddG values calculated for the same mutations using urea
#       denaturation.  These ddG values are in the supplementary table.  I have included them below so that
#       they can be averaged with the DSC values.
D2E 0.0
D9E 1.4
D10E    0.2
D13E    -0.2
D43E    -0.6
D47E    -0.3
D61E    0.6
D104E   0.3
E30D    0.2
E44D    0.6
E48D    1.1
E85D    0.9
E101D   -0.1
I4V 0.3
I5V 0.7
I23V    -0.3
I38V    1.0
I41V    0.7
I45V    0.8
I60V    0.2
I72V    0.0
I75V    0.7
V16I    0.8
V25I    0.9
V55I    0.3
V86I    0.4
V91I    0.1
